BIOL 3702 Lecture Outline

Chapter 19 - Microbial Taxonomy and Phylogeny

Overview

The extraordinary diversity of the microbes is fascinating, yet very complex

Due to the diverse nature of living organisms, it is desirable to categorize them into
groups based upon their similarities

Taxonomy - the science of biological classification

Classification - arrangement of organisms into groups or taxa (s., taxon) based

upon similarities or evolutionary relatedness

Nomenclature - assignment of names to taxonomic groups using special rules
Identification - determining to which recognized taxon a particular organism

belongs

Why is taxonomy important?

Permits the organization of huge amounts of information
Allows predictions and hypotheses to be made upon this information
Places organisms in useful groups with precise names that permit effective

communication between investigators

Essential for the identification of organisms

The term systematics is often used in synonymy with taxonomy

This term is better defined as the scientific study of organisms with the ultimate

object of characterizing and arranging them in an organized manner

Actually encompasses other disciplines including morphology, ecology,

epidemiology, biochemistry, molecular biology, and physiology

Microbial Evolution

Earth is estimated to be 4.6 billion years old

First procaryotic cells, as evident from fossilized remains, appeared about 3.5-3.8
billion years ago and were likely anaerobic

Subsequent evolution of cyanobacteria and oxygenic photosynthesis occurred 2.53.0 billion years ago

Microbial diversity increased as an oxygen-rich environment developed

Carl Woese and colleagues, studying rRNA sequences, suggest that procaryotes
divided into two distinct lineages early in the earths evolution

These workers also suggested that all living things can be placed into one of three
domains

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Chapter 19

Domains - placed above the phylum and kingdom levels of classification

Bacteria - procaryotic
Archaea - procaryotic
Eucarya - eucaryotic

Eucaryotes arose from procaryotes 1.4-2.7 billion years ago

Two hypotheses for the evolution of eucaryotic cells
Organelles arose within procaryotes from the invagination of the plasma

membrane
Endosymbiotic hypothesis
Fusion

of ancient true bacteria and archaea to form a nucleus and a Golgi

apparatus

Mitochondria

and chloroplasts develop later from a permanent symbiotic

relationship with other bacteria, e.g., cyanelle (cyanobacterium) living inside the
protist Cyanophora paradoxa

Taxonomic Ranks

Classification of an organism requires that it be placed (ranked) in a group (taxon)

and given a specific name
Informal names - lactic acid bacterium
Formal names - Lactobacillus acidophilus

Groups are hierarchical in nature

Classification of an organism requires that it be placed (ranked) in a group (taxon)
and given a specific name
Informal names - lactic acid bacterium
Formal names - Lactobacillus acidophilus

Groups are hierarchical in nature

Categories used in any rank unites groups under it based upon common properties
In procaryotes (in ascending order), some ranks have characteristic suffixes
Species (Note: do not capitalize first letter)
Genus
Family (suffix = -aceae)
Order (suffix = -iales)
Class
Phylum
Domain
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Chapter 19

Species - basic taxonomic group

In higher organisms, a species is defined based upon sexual reproduction
Not a good criteria for bacteria - many procaryotes do not reproduce sexually

Procaryotic species - collection of strains that share many stable properties and differ
significantly from other groups of strains

Strain - population of organisms that is distinct from other populations within a

particular taxonomic category and is typically descended from a single organism or a
pure culture
Biovars - biochemical or physiological
Morphovars - shape
Serovars - antigenic properties
Type strain - standard, but not always the most representative member

Genus - a well-defined group of one or more species that is clearly distinct from other
genera

Naming of microbes uses a binomial system developed by Carolus Linnaeus

Genus - Escherichia
Species - coli
Abbreviated - E. coli, but only after the full name/epithet is used once; never start

a sentence with an abbreviation

Classification Systems

Two basic types of classification systems are used:

Phenetic classification
Natural

classification system that groups organisms together based upon

mutual similarity of their phenotypic characteristics

May

be used to infer possible evolutionary relationships

Phylogenetic (phyletic) classification

Based

solely on evolutionary relationships

Has

been difficult to use in the past for procaryotes due to a lack of a fossil
record

Modern

methods instead use gene sequences (e.g., RNA genes) or their

products (proteins) to estimate phylogenetic relationships

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Chapter 19

Taxonomic Characteristics

Classical characteristics
Morphology
Physiological/metabolic
Ecological
Genetic analysis
Transformation
Conjugation
Plasmid

content

Molecular characteristics
Proteins
Sequencing
Physical,

of conserved proteins

kinetic, and regulatory properties

Nucleic acids
Base

composition

Hybridization
Sequencing

of conserved genes, e.g., rRNA because it is generally stable yet

changes over long periods of time

Microbial Phylogeny

There are a number of methods used to assess the phylogeny of microbes

Molecular chronometers - assumes that changes in conversed proteins or genes

occurs over time without destroying or altering the molecules function

Phylogenetic trees - compares molecular sequence differences of a conserved

gene or protein between organisms to generate a tree that expresses the

differences as an evolutionary distance
Signature sequence - particular groups of microbes will possess unique

nucleotides at specific locations in 16S rRNA molecules

Signature sequence - particular groups of microbes will possess unique

nucleotides at specific locations in 16S rRNA molecules

Polyphasic taxonomy - taxonomic scheme which employs a wide range of stable

and accepted phenotypic and genotypic information

Modern microbial taxonomists generally employ phylogenetic trees derived from

rRNA comparisons

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Chapter 19

Divisions of Life

Kingdom systems of classification

Five-kingdom system (Whittaker, 1960s) - based upon cell type, organization, and

the means of nutrient acquisition

Animals
Plants
Fungi

- multicellular eucaryotes, digestion

- multicellular eucaryotes, photosynthesis

- multicellular eucaryotes, absorption

Protista

- unicellular eucaryotes, various methods of nutrition

Monera

- procaryotes

Six-kingdom system - differs from five-kingdom system by dividing procaryotes

into bacteria and archaea

Eight-kingdom system - further division of the protists using rRNA data and

grouping organisms into two empires (Eucaryota and Bacteria) containing a total
of eight kingdoms
Universal/eucaryotic trees - provides for numerous lineages and great diversity

Domain system of classification - based on work of Woese and colleagues using

rRNA to group organisms into three domains
Archaea - procaryotic; differ from Bacteria in cell wall structure, membrane

composition, transfer RNAs, etc. [see details in Table 19.8]

Bacteria - procaryotic
Eucarya - eucaryotic

Bergeys Manual

In 1923, David Bergey and colleagues set out to publish a definitive book on the
identification and classification of bacteria

Bergeys Manuals - the Bibles of bacterial identification/classification

Three versions of these books:
Bergeys Manual of Determinative Bacteriology (currently in its 9th ed.) - species

identification
Bergeys Manual of Systematic Bacteriology, 1st ed. - phenetic system
Bergeys Manual of Systematic Bacteriology, 2nd ed. - phylogenetic system of

classification

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Chapter 19

Survey of the Procaryotes

Bergeys Manual of Systematic Bacteriology (2nd ed.) covers 25 phlya

Bergeys Manual of Systematic Bacteriology (2nd ed.) covers 25 phlya
Groups covered by each volume:
Volume 1
Domain

Archaea

Phylum

Crenarchaeota - thermophylic and hyperthermophylic sulfur

metabolizers

Phylum

Euryarchaeota - methanogens, halophiles, and thermophilic sulfur

reducers

Domain

Bacteria

Phylum

Aquificiae - earliest branch of bacteria that contain autotrophs which

utilize hydrogen for energy production

Phylum

Thermotogae - anaerobic, thermophilic, and fermentative Gramnegative bacteria

Phylum

Deinococcus Thermus - radiation resistant bacteria

Phylum Chloroflexi - green non-sulfur bacteria that carries out anoxygenic

photosynthesis

Phylum

Cyanobacteria - oxygenic photosynthetic bacteria

Phylum

Chlorobi - green sulfur bacteria that carry out anoxygenic

photosynthesis

Volume 2
Proteobacteria
All

- Gram negative

major nutritional types

Five

classes based upon rRNA data

Alphaproteobacteria

- oligotrophic forms including the purple nonsulfur

photosynthesizers
Betaproteobacteria

- metabolically similar to alphaproteobacteria

Gammaproteobacteria
Deltaproteobacteria

- diverse methods of energy metabolism

- includes predators and the fruiting myxobacteria

Epsilonproteobacteria

- contains pathogens

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Chapter 19

Volume 3
Gram-positive
Three

low G+C DNA composition

classes of the phylum Firmicutes

Clostridia

- tend to be anaerobic and endospore formers

Mollicutes

- mycoplasmas (no cell walls)

Bacilli

- Gram-positive aerobes or facultative anaerobes, rods or cocci,

some endospore formers

Volume 4
Gram-positive
All

high G+C DNA composition

belong to the phylum Actinobacteria

Some

are filamentous

Volume 5
Gram-negative
Various
Nine

morphologies

phyla of which four are presented below

Phylum

Planctomycetes - some have a membrane-bound nucleus

Phylum

Chlamydiae - obligate intracellular parasites important in disease

Phylum

Spirochaetes - helical-shaped, Gram-negative motile bacteria (axial

filaments)

Phylum

Bacteroidetes - ecologically significant species are found in this

phylum

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Copyright 2004 by Chester R. Cooper, Jr.